Sure, I'm not saying they are. For myself, XY's problems weren't story based, but rather to do with the pace. The first 30 minutes whizz you from your house to Aquacorde, whilst all of a sudden you have friends and a Pokémon who are more than willing to do just about anything with seconds of meeting them, including getting destroyed by your starter.But a lot of those don't strike me as loose ends as they weren't at all important to the story.
1. Does it matter who they were at war with? From interviews I've read they only included such a huge war to contrast how the pokemon world has changed from the ancient past, the politics of it were not important. And I don't recall any indications of a recent Kalos war.
2. Given it got its own signature move it seems they planned for AZ's Floette to be an event pokemon. As for what it is, its a pokemon mutated by the Ultimate Weapon, similar to how AZ was.
3. The Draconids were an ORAS thing, not Kalos, and is there any reason to think they were anything more than what they were stated to be, namely a secretive group of keepers of ancient knowledge regarding Rayquaza?
4. I'm pretty sure Lysandre's fate would depend on the version, since in one he intends to use the last of the weapon's power to make the group immortal, and in Y version he intends to simply kill them.
5. AZ's brother was a fellow royal and Lysandre's ancestor. If you mean what was his name then that doesn't seem all that important or a loose end.
6. I'm pretty sure one point made during the whole parallel universe story in ORAS is that in the non-mega timeline the Kalos war and Ultimate Weapon never happened, hence why mega stones never became widespread.
But, to play devil's advocate:
1. Well, no, not really, but it's a question many have been pondering seeing as there are no such signs in the real world of any such war taking place in Western Europe, whereas previous plot points have been based on the real world (such as truth vs ideals representing the American Civil War in Unova). And yes, Parfum Palace was built 300 years prior to XY by the respective king of Kalos at that time after victory against neighbouring regions, made even more intriguing by the fact that Zekrom and Reshiram statues reside here alongside a knight with a team of primarily Unovan Pokémon.
2. Here I was speaking more along the lines of "is it supposed to be an ancient example of the Battle Bond phenomenon?" and that kind of thing. It was revived using the life force of other Pokémon; there's nothing to show that it was "mutated" by the weapon, but rather gained the energy of some of the Pokémon sacrificed to give it life.
3. My point was that Rayquaza mega evolved seemingly well before Lucario in Kalos, and from a completely different source of energy (well, arguably). Zinnia speaking about the multiverse and the Draconids seemingly not being around doesn't raise any eyebrows?
4. Well, not really. Regardless of the version, Lysandre's fate is kept under wraps with him not escaping the hideout. Him threatening the player with eternal life/death has no impact on his fate as far as I can remember.
5. Again, i was just bringing up some questions others have had. I don't really see any of these as loose ends per se.
6. Actually, if I recall correctly, the implication was that the war still happened but AZ did not build and use his ultimate weapon (which was the cause of stones being infused with the life energy of dead Pokémon, making them Mega Stones), and that as a result Kalos lost the war and ceased to exist, hence the lack of reference to them in games outside of the Mega Evolution timeline (enforced by the interweaving presence of other regions throughout the core series before this).
I'm with you, though: I don't see the point in returning to a Kalos just for a Zygarde arc or a completion of a revived Flare arc or what-have-you.